4513440c373f2ba57b4d28910e832b4dc85108f5
hiram
  Thu Feb 6 16:53:25 2020 -0800
warn only for liftUp not error out duplicates cause missing refs #23891

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index 5303e5a..6e244a5 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -356,31 +356,31 @@
 fi
 rm -f before.cut9.txt
 
 # extract labels from semi-structured text in gbff COMMENT/description sections:
 zcat \$downloadDir/\${asmId}_rna.gbff.gz \\
   | (grep ' :: ' || true) \\
     | perl -wpe 's/\\s+::.*//; s/^\\s+//;' \\
       | sort -u \\
         > pragmaLabels.txt
 
 # extract cross reference text for refLink
 \$gff3ToRefLink \$downloadDir/\$asmId.raFile.txt \$ncbiGffGz pragmaLabels.txt 2> \$db.refLink.stderr.txt \\
   | sort > \$asmId.refLink.tab
 
 # converting the NCBI coordinates to UCSC coordinates
-liftUp -extGenePred -type=.gp stdout $localLiftFile drop \$asmId.gp \\
+liftUp -extGenePred -type=.gp stdout $localLiftFile warn \$asmId.gp \\
   | gzip -c > \$asmId.\$db.gp.gz
 $genePredCheckDb \$asmId.\$db.gp.gz
 
 # curated subset of all genes
 (zegrep "^[NY][MRP]_" \$asmId.\$db.gp.gz || true) > \$db.curated.gp
 # may not be any curated genes
 if [ ! -s \$db.curated.gp ]; then
   rm -f \$db.curated.gp
 elif [ -s \$asmId.refseqSelectTranscripts.txt ]; then
   cat \$db.curated.gp | fgrep -f \$asmId.refseqSelectTranscripts.txt - \\
     > \$db.refseqSelect.curated.gp
   # may not be any refseqSelect.curated genes
   if [ ! -s \$db.refseqSelect.curated.gp ]; then
     rm -f \$db.refseqSelect.curated.gp
   fi
@@ -421,31 +421,31 @@
   \$db.other.extras.bed \$db.chrom.sizes \$db.other.bb
 
 # Make trix index for ncbiRefSeqOther
 $ncbiRefSeqOtherIxIxx \\
   ncbiRefSeqOther.as \$db.other.extras.bed > ncbiRefSeqOther.ix.tab
 
 ixIxx ncbiRefSeqOther.ix.tab ncbiRefSeqOther.ix{,x}
 
 # PSL data will be loaded into a psl type track to show the alignments
 (zgrep "^#" \$ncbiGffGz | head || true) > gffForPsl.gff
 (zegrep -v "NG_" \$ncbiGffGz || true) \\
   | awk -F\$'\\t' '\$3 == "cDNA_match" || \$3 == "match"' >> gffForPsl.gff
 gff3ToPsl -dropT \$downloadDir/\$asmId.ncbi.chrom.sizes \$downloadDir/rna.sizes \\
   gffForPsl.gff stdout | pslPosTarget stdin \$asmId.psl
 simpleChain -outPsl -maxGap=300000 \$asmId.psl stdout | pslSwap stdin stdout \\
-  | liftUp -type=.psl stdout $localLiftFile drop stdin \\
+  | liftUp -type=.psl stdout $localLiftFile warn stdin \\
    | gzip -c > \$db.psl.gz
 pslCheck $pslTargetSizes \\
    -querySizes=\$downloadDir/rna.sizes \$db.psl.gz
 
 # extract RNA CDS information from genbank record
 # Note: $asmId.raFile.txt could be used instead of _rna.gbff.gz
 \$gbffToCds \$downloadDir/\${asmId}_rna.gbff.gz | sort > \$asmId.rna.cds
 
 # the NCBI _genomic.gff.gz file only contains cDNA_match records for transcripts
 # that do not *exactly* match the reference genome.  For all other transcripts
 # construct 'fake' PSL records representing the alignments of all cDNAs
 # that would be perfect matches to the reference genome.  The pslFixCdsJoinGap
 # will fixup those records with unusual alignments due to frameshifts of
 # various sorts as found in the rna.cds file:
 genePredToFakePsl -qSizes=\$downloadDir/rna.sizes $fakePslSizes \$db \$db.ncbiRefSeq.gp \\